/ (root) | README.md | This README summarizing repo contents and links to external data on GitHub/NIAGADS | Gao Wang |
/variant_gene_summary | — | Summary of variants, loci, and genes annotated by xQTL | — |
├─ /xQTL_loci_summary | — | Summary of xQTL loci | — |
├─ /xQTL_finemapping | UCSC bed.gz | Fine-mapping results, structured into contexts and modalities | — |
├─ /single_context_finemapping | UCSC bed.gz | Per-QTL-type directory containing eQTL, pQTL, sQTL, mQTL, haQTL, caQTL etc. BED files of exported top loci | — |
├─ /multi_context_finemapping | UCSC bed.gz | Multi-context fine-mapping results (e.g., MSBB, ROSMAP) | — |
├─ /multi_gene_finemapping | UCSC bed.gz | Per-QTL-type BED files of top loci aggregated across multiple genes | — |
└─ /trans_finemapping | UCSC bed.gz | Trans fine-mapping BED files, per QTL type and dataset | — |
└─ /xQTL_colocalization | UCSC bed.gz | Colocalization results, structured by multi- and pairwise-context | — |
├─ /multi_context_colocalization | UCSC bed.gz | Multi-context colocalization results | — |
└─ /pairwise_colocalization | UCSC bed.gz / TSV / Misc | Pairwise colocalization results and related files (bulk mQTL haQTL AD etc.) | — |
├─ /AD_loci_summary | — | Summary of Alzheimer’s Disease (AD) loci | — |
├─ /AD_finemapping | UCSC bed.gz | AD GWAS/meta-analysis fine-mapping exported top loci BED files | — |
├─ /AD_colocalization | UCSC bed.gz | AD GWAS/meta-analysis colocalization exported BED files | — |
├─ /AD_xQTL_colocalization | UCSC bed.gz | Integrated AD-xQTL colocalization results | — |
├─ /AD_gene_level | — | AD gene-level results, including TWAS and cTWAS results | — |
├─ /TWAS_MR | UCSC bed.gz | TWAS, cTWAS, Mendelian Randomization summary outputs (large combined files) | Ru Feng (with input from Chunming Liu) |
└─ /cTWAS | UCSC bed.gz | AD cTWAS results | — |
├─ /AD_xQTL_integration_summary | XLSX, TSV | Summary tables for AD loci annotated by xQTL analyses (fine-mapping, colocalization, TWAS, MR) | — |
/xQTL_SCEEM_scores | UCSC bed.gz | ML-based xQTL PIP prediction scores on FTP server | Chirag Lakhani |
/xQTL_GWAS_models | — | Pretrained statistical and ML models for data integration | — |
├─ /xQTL_models | — | xQTL models organized by type | — |
├─ /finemapping_models | RDS | Fine-mapping models by QTL type (eQTL, pQTL, glycoQTL, sQTL) | Ru Feng (main contact) |
├─ /colocalization_models | RDS | Colocalization models | Xuewei Cao |
├─ /TWAS_models | RDS | TWAS models | Ru Feng et al. |
└─ /qTWAS_models | RDS | Quantile TWAS models | Anjing Liu |
├─ /AD_GWAS_models | RDS | AD GWAS fine-mapping and colocalization models | Ruixi Li |
├─ /AD_colocalization | RDS | AD GWAS colocalization models | Ruixi Li |
└─ /AD_finemapping | RDS | AD GWAS fine-mapping models | Ruixi Li |
├─ /AD_xQTL_integration | RDS | AD xQTL integration models | — |
├─ /AD_xQTL_colocalization_models | RDS | AD xQTL colocalization models | — |
└─ /AD_cTWAS_input | RDS | AD cTWAS input data | Chunming Liu |
/xQTL_data (raw pre-release area) | — | Raw xQTL data prior to NIAGADS harmonization; restricted access | — |
├─ /xQTL_LR | UCSC bed.gz (tensorQTL) | Linear regression model data and residual sumstats | Anjing Liu |
├─ /R_lm_residual_sumstats | RDS | Residual summary statistics for linear models | Anjing Liu |
└─ /tensorQTL_sumstats | UCSC bed.gz | Summary statistics from tensorQTL | — |
├─ /xQTL_QR | UCSC bed.gz (tensorQTL) | Quantile regression model data | Anjing Liu |
├─ /xQTL_interaction | UCSC bed.gz (tensorQTL) | Interaction analysis data on HPC and cloud | Anjing Liu |
└─ /xQTL_GLMM | UCSC bed.gz (ISSAC) | Generalized linear mixed model based xQTL calling | Yuntian Zhang, Boxiang Liu |
/reference_files | — | Companion analysis supporting files | — |
├─ /ADSP_LD_reference_data | — | ADSP LD reference data (on Synapse) | Gao Wang |
└─ /EUR | xz (bim format) with meta data | European population LD reference data | Gao Wang |
├─ /LDSC_reference_data | — | LDSC reference files including LD scores and annotations | — |
├─ /LD_scores | Miscellaneous | LD scores data on HPC | Anjing Liu |
├─ /sldsc_annotations | Miscellaneous | S-LDSC annotation files on HPC | Anjing Liu |
├─ /GWAS_munged | Miscellaneous | Munged GWAS summary statistics | Ruixi Li |
├─ /functional_enrichment_annotations | UCSC bed.gz | Functional enrichment annotation files on HPC | Anjing Liu |
└─ /xQTL_protocol_tutorial | Miscellaneous | Toy example and protocol tutorial data compatible with FunGen-xQTL pipeline | Frank Grenn |